If more than 50 genes/sequences are provided as input, then the associated running time can take some time. Therefore it is advisable to provide an email-address in case you are running the Interactive Phylogenetics Module with more than 50 genes. After processing you will be send an email with a link to the created phylogenetic tree.
The selection modi are exclusive: please choose either Gene selection or Species selection.
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":"";
$selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":"";
$num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0;
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ) $local_species = 'acertr' $disabled = '' $selected = ''
include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ) $local_species = 'amhyb' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ) $local_species = 'atr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ) $local_species = 'ath' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ) $local_species = 'arhy' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ) $local_species = 'bol' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ) $local_species = 'bra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ) $local_species = 'camsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ) $local_species = 'cansat' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ) $local_species = 'cru' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ) $local_species = 'cpa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ) $local_species = 'cfa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ) $local_species = 'cil' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ) $local_species = 'ccl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ) $local_species = 'cav' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ) $local_species = 'cme' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ) $local_species = 'csa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ) $local_species = 'dca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ) $local_species = 'dzi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ) $local_species = 'fve' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ) $local_species = 'fan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ) $local_species = 'gma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ) $local_species = 'gra' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ) $local_species = 'han' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ) $local_species = 'lonja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ) $local_species = 'lal' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ) $local_species = 'mbi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ) $local_species = 'pvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ) $local_species = 'pgr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ) $local_species = 'qlo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ) $local_species = 'rch' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ) $local_species = 'stu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ) $local_species = 'tpr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ) $local_species = 'tar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ), 'gf_id' => 'HOM05D001218', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001218' ), 'data_identifier' => 'HOM05D001218', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001218', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '514', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A06p09480' => 'bna', 'A06p16940' => 'bna', 'A07p42210' => 'bna', 'A08p29140' => 'bna', 'A08p33100' => 'bna', 'A08p33110' => 'bna', 'A09p26530' => 'bna', 'Aa31LG1G2740' => 'aar', 'Aa31LG7G5130' => 'aar', 'Aa31LG9G9920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.4948' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5184' => 'aag', 'Actinidia02341' => 'ach', 'Actinidia13737' => 'ach', 'Actinidia15552' => 'ach', 'Actinidia17088' => 'ach', 'Actinidia30977' => 'ach', 'Actinidia37903' => 'ach', 'Ah.14g087830' => 'amhyb', 'AL1G33980' => 'aly', 'AL2G36690' => 'aly', 'Aqoxy1G04195' => 'aox', 'Aqoxy4G01055' => 'aox', 'Aqoxy5G00952' => 'aox', 'arahy.Tifrunner.gnm1.ann1.A89GZ1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BFE9YH' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GJ5TV3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GMWI1E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H559FZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H5UTXB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J9WPR7' => 'arhy', 'AT1G12000' => 'ath', 'AT1G20950' => 'ath', 'AT1G76550' => 'ath', 'AT4G04040' => 'ath', 'AT4G08876' => 'ath', 'ATR0026G007' => 'atr', 'ATR0057G131' => 'atr', 'ATR0605G031' => 'atr', 'Atru.chr10.2329' => 'acertr', 'Atru.chr10.2330' => 'acertr', 'Atru.chr13.35' => 'acertr', 'Atru.chr6.3243' => 'acertr', 'Atru.chr8.848' => 'acertr', 'AUR62012760' => 'cqu', 'AUR62013305' => 'cqu', 'AUR62021897' => 'cqu', 'AUR62035185' => 'cqu', 'AUR62043319' => 'cqu', 'BcaB01g01783' => 'bca', 'BcaB01g01786' => 'bca', 'BcaB02g06436' => 'bca', 'BcaB03g12841' => 'bca', 'BcaB07g32089' => 'bca', 'BcaB08g37436' => 'bca', 'BcaB08g37437' => 'bca', 'BcaC04g21267' => 'bca', 'BcaC05g25234' => 'bca', 'BcaC05g26002' => 'bca', 'BcaC07g39066' => 'bca', 'BcaC07g40596' => 'bca', 'BcaC07g40644' => 'bca', 'BcaC07g41739' => 'bca', 'BcaC07g41740' => 'bca', 'BcaC07g41742' => 'bca', 'BcaC07g41743' => 'bca', 'BcaC07g41755' => 'bca', 'BcaC08g47163' => 'bca', 'BcaC08g47232' => 'bca', 'BolC4t24726H' => 'bol', 'BolC5t29865H' => 'bol', 'BolC5t30663H' => 'bol', 'BolC6t40103H' => 'bol', 'BolC7t42081H' => 'bol', 'BolC8t49142H' => 'bol', 'BolC8t49679H' => 'bol', 'BolC8t52318H' => 'bol', 'BolC9t56199H' => 'bol', 'BraA06t24135Z' => 'bra', 'BraA06t24804Z' => 'bra', 'BraA07t31750Z' => 'bra', 'BraA08t34850Z' => 'bra', 'BraA08t35229Z' => 'bra', 'BraA09t38226Z' => 'bra', 'BraA10t43274Z' => 'bra', 'C02p24130' => 'bna', 'C03p79150' => 'bna', 'C03p79160' => 'bna', 'C04p31780' => 'bna', 'C05p11190' => 'bna', 'C05p19600' => 'bna', 'C06p50810' => 'bna', 'C07p15890' => 'bna', 'C08p15120' => 'bna', 'C08p20520' => 'bna', 'C08p47780' => 'bna', 'C09p33650' => 'bna', 'CAN.G1014.50' => 'can', 'CAN.G1330.23' => 'can', 'CAN.G208.42' => 'can', 'CAN.G664.3' => 'can', 'CANSAT25G3586' => 'cansat', 'CANSAT56G0463' => 'cansat', 'CARHR012330' => 'chi', 'CARHR021410' => 'chi', 'CARHR070100' => 'chi', 'CARHR253400' => 'chi', 'Carub.0001s1168' => 'cru', 'Carub.0001s2042' => 'cru', 'Carub.0002s2346' => 'cru', 'Carub.0006s3207' => 'cru', 'Ca_00697_v3' => 'car', 'Ca_12496_v3' => 'car', 'Ca_21059_v3' => 'car', 'CBR_g3137' => 'cbr', 'CBR_g3138' => 'cbr', 'CBR_g6623' => 'cbr', 'Cc02_g26170' => 'ccan', 'Cc05_g03150' => 'ccan', 'Cc09_g01150' => 'ccan', 'CDE04G0741' => 'cde', 'CDE05G0435' => 'cde', 'CDE05G0891' => 'cde', 'CDE07G0059' => 'cde', 'CDE10G0658' => 'cde', 'Cfa000157' => 'cfa', 'Cfa014150' => 'cfa', 'Cfa014326' => 'cfa', 'Ciclev10000595m.g' => 'ccl', 'Ciclev10013226m.g' => 'ccl', 'Ciclev10014750m.g' => 'ccl', 'Ciclev10014760m.g' => 'ccl', 'Ciclev10017788m.g' => 'ccl', 'CiPaw.07G074600' => 'cil', 'CiPaw.07G131800' => 'cil', 'CiPaw.08G078100' => 'cil', 'CiPaw.09G098500' => 'cil', 'CiPaw.10G074900' => 'cil', 'ClCG01G009730' => 'cla', 'ClCG01G021630' => 'cla', 'ClCG09G001500' => 'cla', 'ClCG11G019100' => 'cla', 'COL.COLO4_00111' => 'col', 'COL.COLO4_03406' => 'col', 'COL.COLO4_30953' => 'col', 'COL.COLO4_31836' => 'col', 'Cpa.g.c24967.5' => 'cpa', 'Cpa.g.sc1180.1' => 'cpa', 'CsaV3_1G046070' => 'csa', 'CsaV3_4G037690' => 'csa', 'CsaV3_6G048680' => 'csa', 'CsaV3_7G033830' => 'csa', 'CSS0003035' => 'camsi', 'CSS0013185' => 'camsi', 'CSS0017591' => 'camsi', 'CSS0039251' => 'camsi', 'DCAR_002206' => 'dca', 'DCAR_012926' => 'dca', 'DCAR_013949' => 'dca', 'DCAR_017621' => 'dca', 'DCAR_027859' => 'dca', 'DCAR_030888' => 'dca', 'Dinv13942' => 'din', 'Dinv20110' => 'din', 'Dinv23340' => 'din', 'Dinv39742' => 'din', 'Dinv43989' => 'din', 'Duzib093G2014' => 'dzi', 'Duzib116G0454' => 'dzi', 'Duzib133G0191' => 'dzi', 'Duzib192G0358' => 'dzi', 'Duzib235G1138' => 'dzi', 'Duzib235G1528' => 'dzi', 'ECA232G2106' => 'eca', 'ECA233G0383' => 'eca', 'ECA233G4050' => 'eca', 'ECA233G6219' => 'eca', 'ECA234G4191' => 'eca', 'EL10Ac1g01822' => 'bvu', 'EL10Ac8g20133' => 'bvu', 'Eucgr.E01760' => 'egr', 'Eucgr.E03983' => 'egr', 'Eucgr.F01823' => 'egr', 'Eucgr.F03611' => 'egr', 'Eucgr.K00768' => 'egr', 'FAN02G0520' => 'fan', 'FAN02G3767' => 'fan', 'FAN04G0409' => 'fan', 'FAN05G5283' => 'fan', 'FAN08G1986' => 'fan', 'FAN09G1873' => 'fan', 'FAN13G0530' => 'fan', 'FAN14G3074' => 'fan', 'FAN16G2361' => 'fan', 'FAN18G2420' => 'fan', 'FAN25G3460' => 'fan', 'FvH4_3g01360' => 'fve', 'FvH4_5g26380' => 'fve', 'FvH4_6g42470' => 'fve', 'Glyma.02G169400' => 'gma', 'Glyma.07G160500' => 'gma', 'Glyma.07G263800' => 'gma', 'Glyma.09G007900' => 'gma', 'Glyma.10G128200' => 'gma', 'Glyma.14G096300' => 'gma', 'Glyma.15G112300' => 'gma', 'Glyma.17G010100' => 'gma', 'Glyma.20G007400' => 'gma', 'Gohir.A02G087100' => 'ghi', 'Gohir.A06G141380' => 'ghi', 'Gohir.A06G151500' => 'ghi', 'Gohir.A10G010800' => 'ghi', 'Gohir.A11G153500' => 'ghi', 'Gohir.D02G101900' => 'ghi', 'Gohir.D06G145600' => 'ghi', 'Gohir.D06G157700' => 'ghi', 'Gohir.D10G010500' => 'ghi', 'Gohir.D11G160300' => 'ghi', 'Gorai.005G115600' => 'gra', 'Gorai.007G170900' => 'gra', 'Gorai.010G169500' => 'gra', 'Gorai.010G184300' => 'gra', 'Gorai.011G011600' => 'gra', 'GSVIVG01004820001' => 'vvi', 'GSVIVG01013442001' => 'vvi', 'GSVIVG01026761001' => 'vvi', 'GSVIVG01030491001' => 'vvi', 'HanXRQChr01g0006531' => 'han', 'HanXRQChr01g0006541' => 'han', 'HanXRQChr05g0161401' => 'han', 'HanXRQChr08g0216771' => 'han', 'HanXRQChr09g0254551' => 'han', 'HanXRQChr10g0310151' => 'han', 'HanXRQChr12g0365701' => 'han', 'HanXRQChr13g0410351' => 'han', 'HanXRQChr14g0427931' => 'han', 'HanXRQChr16g0512491' => 'han', 'HanXRQChr16g0516901' => 'han', 'HanXRQChr17g0558271' => 'han', 'Haze_06862' => 'cav', 'Haze_12778' => 'cav', 'Haze_22874' => 'cav', 'Hma1.2p1_0005F.1_g004330' => 'hma', 'Hma1.2p1_0450F.1_g155500' => 'hma', 'Hma1.2p1_0489F.1_g164180' => 'hma', 'Hma1.2p1_0810F.1_g221990' => 'hma', 'Hma1.2p1_1064F.1_g253630' => 'hma', 'Hma1.2p1_1530F.1_g289220' => 'hma', 'HPP92_002587' => 'vpl', 'HPP92_003839' => 'vpl', 'HPP92_003843' => 'vpl', 'HPP92_007461' => 'vpl', 'HPP92_017265' => 'vpl', 'HPP92_017280' => 'vpl', 'Hund01814' => 'sun', 'Hund01816' => 'sun', 'Hund01817' => 'sun', 'Hund21438' => 'sun', 'Hund23428' => 'sun', 'Lalb_Chr04g0258861' => 'lal', 'Lalb_Chr10g0095321' => 'lal', 'Lalb_Chr12g0196021' => 'lal', 'Lalb_Chr15g0087821' => 'lal', 'Lalb_Chr17g0338171' => 'lal', 'Lalb_Chr18g0056801' => 'lal', 'Lj1A779G43' => 'lonja', 'Lj1C1236G16' => 'lonja', 'Lj2C264T4' => 'lonja', 'Lj2g0017094' => 'lja', 'Lj4C3G12' => 'lonja', 'Lj4g0017898' => 'lja', 'Lj4g0019624' => 'lja', 'Lj6g0002654' => 'lja', 'Lsat_1_v5_gn_0_27020' => 'lsa', 'Lsat_1_v5_gn_2_3161' => 'lsa', 'Lsat_1_v5_gn_4_61761' => 'lsa', 'Lsat_1_v5_gn_5_56700' => 'lsa', 'Lsat_1_v5_gn_8_26721' => 'lsa', 'Lsat_1_v5_gn_9_106661' => 'lsa', 'Lsat_1_v5_gn_9_48180' => 'lsa', 'Manes.05G129500' => 'mes', 'Manes.08G067100' => 'mes', 'Manes.16G002600' => 'mes', 'Manes.17G026900' => 'mes', 'Manes.18G001100' => 'mes', 'Mapoly0068s0100' => 'mpo', 'Mapoly0105s0043' => 'mpo', 'MBI01_g22962_MAGBIO' => 'mbi', 'MBI01_g45278_MAGBIO' => 'mbi', 'MBI04_g22928_MAGBIO' => 'mbi', 'MBI04_g42538_MAGBIO' => 'mbi', 'MBI17_g33116_MAGBIO' => 'mbi', 'MBI18_g13002_MAGBIO' => 'mbi', 'MBI19_g39687_MAGBIO' => 'mbi', 'MBI19_g41379_MAGBIO' => 'mbi', 'MCO05G307' => 'mco', 'MD05G1352800' => 'mdo', 'MD05G1353200' => 'mdo', 'MD05G1354600' => 'mdo', 'MD05G1354700' => 'mdo', 'MD05G1354900' => 'mdo', 'MD06G1002300' => 'mdo', 'MD09G1112800' => 'mdo', 'MD10G1327400' => 'mdo', 'Medtr1g035230' => 'mtr', 'Medtr2g025020' => 'mtr', 'Medtr4g132700' => 'mtr', 'MELO3C007421.2' => 'cme', 'MELO3C017063.2' => 'cme', 'MELO3C021720.2' => 'cme', 'MELO3C024296.2' => 'cme', 'Migut.C00344' => 'egut', 'Migut.H01592' => 'egut', 'Migut.M01367' => 'egut', 'Migut.N02993' => 'egut', 'MSTRG.1008' => 'ama', 'MSTRG.13127' => 'ama', 'MSTRG.16007' => 'ama', 'MSTRG.24523' => 'ama', 'MSTRG.24899' => 'ama', 'MSTRG.7184' => 'ama', 'Nitab4.5_0000464g0120' => 'nta', 'Nitab4.5_0000482g0220' => 'nta', 'Nitab4.5_0001309g0150' => 'nta', 'Nitab4.5_0003423g0060' => 'nta', 'Nitab4.5_0003449g0050' => 'nta', 'Nitab4.5_0006125g0020' => 'nta', 'Nitab4.5_0012958g0010' => 'nta', 'Nn1g03386' => 'nnu', 'Nn1g07280' => 'nnu', 'Nn1g08050' => 'nnu', 'Nn5g31069' => 'nnu', 'Nn6g31597' => 'nnu', 'Oeu005202.1' => 'oeu', 'Oeu007155.1' => 'oeu', 'Oeu035767.1' => 'oeu', 'Oeu042498.1' => 'oeu', 'Oeu051377.1' => 'oeu', 'Oeu051880.1' => 'oeu', 'Oeu064732.1' => 'oeu', 'Os02g0714200' => 'osa', 'Os06g0247500' => 'osa', 'Os06g0326400' => 'osa', 'Os08g0345700' => 'osa', 'Os09g0298100' => 'osa', 'Peaxi162Scf00064g01432' => 'pax', 'Peaxi162Scf00385g00622' => 'pax', 'Peaxi162Scf00708g00011' => 'pax', 'Peaxi162Scf00921g00255' => 'pax', 'PGR004G1061' => 'pgr', 'PGR031G3703' => 'pgr', 'PGR042G1532' => 'pgr', 'PGSC0003DMG400010007' => 'stu', 'PGSC0003DMG400016726' => 'stu', 'PGSC0003DMG400029309' => 'stu', 'PGSC0003DMG401000669' => 'stu', 'Phvul.003G009600' => 'pvu', 'Phvul.003G082000' => 'pvu', 'Phvul.004G111200' => 'pvu', 'Phvul.006G145300' => 'pvu', 'Phvul.008G128600' => 'pvu', 'Potri.002G003100' => 'ptr', 'Potri.004G003800' => 'ptr', 'Potri.005G257800' => 'ptr', 'Potri.006G024500' => 'ptr', 'Potri.006G281900' => 'ptr', 'Potri.010G106950' => 'ptr', 'Potri.011G015600' => 'ptr', 'Potri.011G015900' => 'ptr', 'Pp3c15_2400' => 'ppa', 'Pp3c18_9850' => 'ppa', 'Pp3c1_39460' => 'ppa', 'Pp3c21_16140' => 'ppa', 'Pp3c2_11980' => 'ppa', 'Pp3c9_5850' => 'ppa', 'Prupe.3G211800' => 'ppe', 'Prupe.4G014600' => 'ppe', 'Prupe.5G003400' => 'ppe', 'Psat0s2691g0160' => 'psa', 'Psat0s5519g0040' => 'psa', 'Psat0s905g0040' => 'psa', 'Psat1g072640' => 'psa', 'Psat1g136120' => 'psa', 'Psat1g159120' => 'psa', 'Psat1g159440' => 'psa', 'Psat2g088600' => 'psa', 'Psat2g088640' => 'psa', 'Psat2g090360' => 'psa', 'Psat2g099920' => 'psa', 'Psat4g004440' => 'psa', 'Psat4g125680' => 'psa', 'Psat6g112440' => 'psa', 'Psat6g112480' => 'psa', 'Psat6g131840' => 'psa', 'Psat7g194800' => 'psa', 'PSO017G6550' => 'pso', 'PSO170G0003' => 'pso', 'PSO210G1993' => 'pso', 'PSO210G6488' => 'pso', 'PSO478G2179' => 'pso', 'PSO541G4791' => 'pso', 'PSO675G8324' => 'pso', 'QL02p016004' => 'qlo', 'QL05p071720' => 'qlo', 'RcHm_v2.0_Chr1g0337721' => 'rch', 'RcHm_v2.0_Chr2g0158381' => 'rch', 'RcHm_v2.0_Chr4g0419181' => 'rch', 'RcHm_v2.0_Chr5g0001981' => 'rch', 'RcHm_v2.0_Chr7g0217221' => 'rch', 'Rhsim06G0002000' => 'rsi', 'Rhsim06G0166600' => 'rsi', 'Rhsim13G0149800' => 'rsi', 'Sabra02G0002000' => 'sbr', 'Sabra05G0199700' => 'sbr', 'Sabra06G0017900' => 'sbr', 'Sabra11G0008700' => 'sbr', 'Sabra11G0010300' => 'sbr', 'Sabra11G0011800' => 'sbr', 'Sabra11G0012000' => 'sbr', 'SalBow1G8581' => 'sbo', 'SalBow8G0814' => 'sbo', 'Sc02g0009320' => 'sci', 'Sc05g0009460' => 'sci', 'Sed0002104' => 'sed', 'Sed0007879' => 'sed', 'Sed0008689' => 'sed', 'Sed0013544' => 'sed', 'Sed0027532' => 'sed', 'Sed0027902' => 'sed', 'SEGI_06789' => 'sgi', 'SEGI_09525' => 'sgi', 'SEGI_18001' => 'sgi', 'SEGI_33302' => 'sgi', 'SGA_v2.0_scaffold161G37861' => 'sas', 'SGA_v2.0_scaffold200G41306' => 'sas', 'SGA_v2.0_scaffold222G42792' => 'sas', 'SGA_v2.0_scaffold227G43178' => 'sas', 'SGA_v2.0_scaffold38G14980' => 'sas', 'SGA_v2.0_scaffold4G01897' => 'sas', 'SGA_v2.0_scaffold73G24447' => 'sas', 'SGA_v2.0_scaffold7G03787' => 'sas', 'SGA_v2.0_scaffold94G28545' => 'sas', 'SMO115G0046' => 'smo', 'SMO270G0037' => 'smo', 'Solyc02g081160.3' => 'sly', 'Solyc04g026340.2' => 'sly', 'Solyc04g082880.4' => 'sly', 'Solyc07g049280.3' => 'sly', 'Solyc12g095760.2' => 'sly', 'Sopen02g025800' => 'spe', 'Sopen04g015280' => 'spe', 'Sopen04g036520' => 'spe', 'Sopen07g024610' => 'spe', 'Sopen12g031660' => 'spe', 'Sp1g10670' => 'spa', 'Sp1g18650' => 'spa', 'Sp5g31710' => 'spa', 'Sp6g04690' => 'spa', 'TAR375G0723' => 'tar', 'TAR376G0228' => 'tar', 'TAR624G0763' => 'tar', 'TAR625G0052' => 'tar', 'TAR626G0797' => 'tar', 'TAR627G0065' => 'tar', 'TAR627G0945' => 'tar', 'TAR628G0316' => 'tar', 'TAR629G1021' => 'tar', 'THA.LOC104804960' => 'tha', 'THA.LOC104806322' => 'tha', 'THA.LOC104809476' => 'tha', 'THA.LOC104809665' => 'tha', 'THA.LOC104812017' => 'tha', 'THA.LOC104813730' => 'tha', 'THA.LOC104818616' => 'tha', 'Thecc.01G180900' => 'tca', 'Thecc.06G138500' => 'tca', 'Thecc.06G228800' => 'tca', 'Thecc.08G098300' => 'tca', 'Thhalv10007087m.g' => 'esa', 'Thhalv10007237m.g' => 'esa', 'Thhalv10018291m.g' => 'esa', 'Thhalv10028543m.g' => 'esa', 'TPR.G13139' => 'tpr', 'TPR.G13926' => 'tpr', 'TPR.G17655' => 'tpr', 'TPR.G18596' => 'tpr', 'TPR.G37001' => 'tpr', 'TPR.G37098' => 'tpr', 'TWI12G0956' => 'twi', 'TWI36G0968' => 'twi', 'TWI38G0213' => 'twi', 'TWI75G0735' => 'twi', 'unitig_61.g26096' => 'ugi', 'unitig_62.g23507' => 'ugi', 'vmacro03661' => 'vma', 'vmacro21744' => 'vma', 'VMungo0540G0252' => 'vmu', 'VMungo1215G1801' => 'vmu', 'VMungo1215G2156' => 'vmu', 'VMungo1215G2664' => 'vmu', 'Zm00001eb043000' => 'zma', 'Zm00001eb153820' => 'zma', 'Zm00001eb188910' => 'zma', 'Zm00001eb252630' => 'zma', 'Zm00001eb273400' => 'zma', 'Zm00001eb280120' => 'zma', 'Zm00001eb281610' => 'zma', 'Zm00001eb309240' => 'zma', 'Zm00001eb321510' => 'zma', 'Zm00001eb321520' => 'zma', 'Zm00001eb354160' => 'zma', 'Zm00001eb358830' => 'zma', 'Zm00001eb371740' => 'zma', 'Zm00001eb381920' => 'zma' ) $gf_id = 'HOM05D001218' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001218' ) $data_identifier = 'HOM05D001218' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 19, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 1, 'aly' => (int) 2, 'aox' => (int) 3, 'arhy' => (int) 7, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 20, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 3, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 5, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 4, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 5, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 1, 'mdo' => (int) 8, 'mtr' => (int) 3, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 7, 'nnu' => (int) 5, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 5, 'ptr' => (int) 8, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 17, 'pso' => (int) 7, 'qlo' => (int) 2, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 7, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 9, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 7, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb381920' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1